[phenixbb] Map quality

Smith Liu smith_liu123 at 163.com
Sun May 17 01:07:37 PDT 2015

For example, can we use the phenix cut out density and then treat the phenix cut out density maps (all in mtz) from different sources (ccp4 or mtz) as comparable from the view of sigmal level?

At 2015-05-17 03:28:06, "Murpholino Peligro" <murpholinox at gmail.com> wrote:

So...Is there a tool/program/formula to get equivalent sigma levels between maps so they can be compared?

2015-05-15 11:37 GMT-05:00 Pavel Afonine <pafonine at lbl.gov>:
Hi Mohamed,

this is not a simple topic.. Two texts I suggest to have a look at are listed below I'm sure there are more). They may not give you a quick solution but perhaps will explain the issues.

Acta Cryst. (2014). D70, 2593-2606
Metrics for comparison of crystallographic maps

Acta Cryst. (2015). D71, 646-666.
FEM: feature-enhanced map

In a very nutshell,

- "1 sigma (or any other x sigma) level for one map may not be the same as 1 sigma (or any other x sigma) level for another map";
- Think of "global vs local". Somehow you need to quantify map quality locally.
- Map correlation (RSCC or map CC, for alternative names) may be a misleading metric is used without care: for example, two poor but similar map may give you high CC.

All the best,

On 5/15/15 9:10 AM, mohamed noor wrote:
Dear all

Is there a single (or a few) metrics that can be used to quantitatively assess map quality instead of looking at each one in Coot? For example, I want to compare the effect of having low completeness in the low resolution shells.


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